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molecular-optimization

Iterative lead optimization with analyze-reason-generate-verify-evaluate loop. Paper-backed (MT-Mol, DrugR, MultiMol).

backend/cli/skills/chemistry/molecular-optimization/SKILL.md

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# Molecular Optimization

## Overview

Lead optimization is the bottleneck of drug discovery — modifying a hit compound to improve potency, selectivity, and ADMET properties without breaking what already works. LLMs frequently generate invalid SMILES or propose modifications that don't appear in the actual structure.

This skill implements an iterative optimization protocol based on three peer-reviewed approaches:
- **MT-Mol** (Kim et al., 2025): Multi-agent tool-based reasoning with verification — SOTA on 17/23 PMO benchmark tasks
- **DrugR** (Liu et al., 2026): Explicit liability reasoning before generation — 18× improvement over blind generation
- **MultiMol** (Yu et al., 2025): Generate-then-rank with scaffold preservation — 82.3% multi-objective success rate

The core loop: **Analyze → Identify Liabilities → Generate Candidates → Verify → Evaluate & Rank → Iterate**.

## When to Use This Skill